delayed walking... possible cause of hypothyroidism???

When my son was born his screening test for T4/TSH came back abnormal.  We were told in the hospital that his T4 was low and they referred us to a pediatric endocrinologist.  The specialist prescribed some blood work and she said that even though his T4 is low he had no hypothyroidism.  these are the results when he was 29 days old
IGF-BP3    1.7
T4, Free (Direct) 1.36
Insulin- Like growth factor-1 86
TSH 2.049
Thryoxine Binding Globulin <4

What do these results mean? Was the endocrinologist right in saying he doesn’t have hypothyroidism?

Even though we believed her and went on with our lives, the reason I am asking for advice now, is that my son is almost 2 years now and he has been diagnosed with low muscle tone in his legs and lower trunk muscles.  He walked at almost 22 months, and we are wondering if it’s possible that the abnormal T4 has anything to do with this.
We took him to a pediatric neurologist when he was 20 months and this was her impression:
Delayed walking, decreased muscle tone and bulk predominantly involving lower extremities, diminished deep tendon reflexes-suggestive of weakness of peripheral neuromuscular origin, anterior horn cell disease such as spinal muscular atrophy suspected.  
The CK results came back normal but we are still waiting for the SMA results.  We started him on physical therapy when he was 21 months.  He started walking a month after we started physical therapy and even though he is showing signs of improvement we are concerned because he falls a lot and has poor balance on his hips.  Any advice or recommendations are welcome; please we are really concerned and are willing to try everything just to get him better.